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Search Results: 1 - 10 of 179210 matches for " Stéphane de Palmas "
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Coverage, Diversity, and Functionality of a High-Latitude Coral Community (Tatsukushi, Shikoku Island, Japan)
Vianney Denis, Takuma Mezaki, Kouki Tanaka, Chao-Yang Kuo, Stéphane De Palmas, Shashank Keshavmurthy, Chaolun Allen Chen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054330
Abstract: Background Seawater temperature is the main factor restricting shallow-water zooxanthellate coral reefs to low latitudes. As temperatures increase, coral species and perhaps reefs may move into higher-latitude waters, increasing the chances of coral reef ecosystems surviving despite global warming. However, there is a growing need to understand the structure of these high-latitude coral communities in order to analyze their future dynamics and to detect any potential changes. Methodology/Principal Findings The high-latitude (32.75°N) community surveyed was located at Tatsukushi, Shikoku Island, Japan. Coral cover was 60±2% and was composed of 73 scleractinian species partitioned into 7 functional groups. Although only 6% of species belonged to the ‘plate-like’ functional group, it was the major contributor to species coverage. This was explained by the dominance of plate-like species such as Acropora hyacinthus and A. solitaryensis. Comparison with historical data suggests a relatively recent colonization/development of A. hyacinthus in this region and a potential increase in coral diversity over the last century. Low coverage of macroalgae (2% of the benthic cover) contrasted with the low abundance of herbivorous fishes, but may be reasonably explained by the high density of sea urchins (12.9±3.3 individuals m?2). Conclusions/Significance The structure and composition of this benthic community are relatively remarkable for a site where winter temperature can durably fall below the accepted limit for coral reef development. Despite limited functionalities and functional redundancy, the current benthic structure might provide a base upon which a reef could eventually develop, as characterized by opportunistic and pioneer frame-building species. In addition to increasing seawater temperatures, on-going management actions and sea urchin density might also explain the observed state of this community. A focus on such ‘marginal’ communities should be a priority, as they can provide important insights into how tropical corals might cope with environmental changes.
Fast Growth May Impair Regeneration Capacity in the Branching Coral Acropora muricata
Vianney Denis, Mireille M. M. Guillaume, Madeleine Goutx, Stéphane de Palmas, Julien Debreuil, Andrew C. Baker, Roxane K. Boonstra, J. Henrich Bruggemann
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072618
Abstract: Regeneration of artificially induced lesions was monitored in nubbins of the branching coral Acropora muricata at two reef-flat sites representing contrasting environments at Réunion Island (21°07′S, 55°32′E). Growth of these injured nubbins was examined in parallel, and compared to controls. Biochemical compositions of the holobiont and the zooxanthellae density were determined at the onset of the experiment, and the photosynthetic efficiency (Fv/Fm) of zooxanthellae was monitored during the experiment. Acropora muricata rapidly regenerated small lesions, but regeneration rates significantly differed between sites. At the sheltered site characterized by high temperatures, temperature variations, and irradiance levels, regeneration took 192 days on average. At the exposed site, characterized by steadier temperatures and lower irradiation, nubbins demonstrated fast lesion repair (81 days), slower growth, lower zooxanthellae density, chlorophyll a concentration and lipid content than at the former site. A trade-off between growth and regeneration rates was evident here. High growth rates seem to impair regeneration capacity. We show that environmental conditions conducive to high zooxanthellae densities in corals are related to fast skeletal growth but also to reduced lesion regeneration rates. We hypothesize that a lowered regenerative capacity may be related to limited availability of energetic and cellular resources, consequences of coral holobionts operating at high levels of photosynthesis and associated growth.
EggLib: processing, analysis and simulation tools for population genetics and genomics
Stéphane De Mita, Mathieu Siol
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-27
Abstract: In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications.EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ webcite where a full documentation and a manual can also be found and downloaded.The exponential growth of sequence databases and the advent of powerful and cost-efficient sequencing technologies have boosted the field of molecular population genetics, providing researchers with an unprecedented and ever growing amount of data [1]. Computing resources appear to be frequently limiting, complicating or even preventing the application of certain analytical methods. To overcome such limitations, automated analysis procedures and efficient computational tools are required.Although a number of programs and pieces of software implement various tasks routinely performed by population geneticists, few stand-alone packages or libraries gather together a la
A simple and efficient model for mesoscale solidification simulation of globular grain structures
Stéphane Vernède,Michel Rappaz
Physics , 2007, DOI: 10.1016/j.actamat.2006.10.031
Abstract: A simple model for the solidification of globular grains in metallic alloys is presented. Based on the Voronoi diagram of the nuclei centers, it accounts for the curvature of the grains near triple junctions. The predictions of this model are close to those of more refined approaches such as the phase field method, but with a computation cost decreased by several orders of magnitude. Therefore, this model is ideally suited for granular simulations linking the behavior of individual grains to macroscopic properties of the material.
Time-resolved and spectral-resolved optical imaging to study brain hemodynamics in songbirds
Stéphane Mottin,Bruno Montcel,Hugues Guillet De Chatellus,Stéphane Ramstein,Clémentine Vignal
Quantitative Biology , 2014, DOI: 10.1117/12.889799
Abstract: Contrary to the intense debate about brain oxygen dynamics and its uncoupling in mammals, very little is known in birds. In zebra finches, picosecond optical tomography (POT) with a white laser and a streak camera can measure in vivo oxy-hemoglobin (HbO2) and deoxy-hemoglobin (Hb) concentration changes following physiological stimulation (familiar calls and songs). POT demonstrated sufficient sub-micromolar sensitivity to resolve the fast changes in hippocampus and auditory forebrain areas with 250 \mu m resolution. The time-course is composed of (i) an early 2s-long event with a significant decrease in Hb and HbO2, respectively -0.7 \mu Moles/L and -0.9 \mu Moles/L (ii) a subsequent increase in blood oxygen availability with a plateau of HbO2 (+0.3 \mu Moles/L) and (iii) pronounced vasodilatation events immediately following the end of the stimulus. One of the findings of our work is the direct link between the blood oxygen level-dependent (BOLD) signals previously published in birds and our results. Furthermore, the early vasoconstriction event and post-stimulus ringing seem to be more pronounced in birds than in mammals. These results in bird, a tachymetabolic vertebrate with a long lifespan, can potentially yield new insights for example in brain aging.
Pricing and Hedging in Stochastic Volatility Regime Switching Models  [PDF]
Stéphane Goutte
Journal of Mathematical Finance (JMF) , 2013, DOI: 10.4236/jmf.2013.31006

We consider general regime switching stochastic volatility models where both the asset and the volatility dynamics depend on the values of a Markov jump process. Due to the stochastic volatility and the Markov regime switching, this financial market is thus incomplete and perfect pricing and hedging of options are not possible. Thus, we are interested in finding formulae to solve the problem of pricing and hedging options in this framework. For this, we use the local risk minimization approach to obtain pricing and hedging formulae based on solving a system of partial differential equations. Then we get also formulae to price volatility and variance swap options on these general regime switching stochastic volatility models.


Feed Signal Influence and Potential Performances of a Compact Radiation Source Based on a Helical Antenna  [PDF]
Laurent Pecastaing, Marc Rivaletto, Antoine de Ferron, Romain Pecquois, René Vézinet, Jean-Christophe Diot, Stéphane Tortel
Journal of Electromagnetic Analysis and Applications (JEMAA) , 2015, DOI: 10.4236/jemaa.2015.77021
Abstract: In the class of emerging high power electromagnetic sources, a complete pulsed power source, named MOUNA (French acronym of “Module Oscillant Utilisant une Nouvelle Architecture”) has been developed. This device must transmit waveforms with a wide frequency band and a high figure-of-merit. To improve the overall performance of the MOUNA system while maintaining its compact size, two approaches are being explored in the paper: the replacement of the dipole antenna by a helical antenna and its feeding signal influence. Helical antenna is cylindrical shape and relatively compact. It offers relatively good gain factor and directivity. The waveform delivered to the antenna is directly related to the amplitude of the radiated electric field. Therefore, different waveforms (step pulse, Gaussian pulse, bipolar pulse and damped sinusoid) are compared to point out the feed signal influence on the radiated electric field. Switch oscillators appear to be considered as interesting resonant sources for driving an antenna. The novel radiating source consists of a primary power source, a resonant transformer, a coaxial transmission line damped oscillator (also termed as coaxial resonator), and a helical antenna. This high voltage pulsed source is very compact (volume of only 2500 cc without the antenna). Our study aims at designing the antenna (number of turns, size…) and a coaxial damped oscillator directly implemented at the output of the transformer. A CST-based simulation is proposed to predict the performances of this wideband source.
Characteristics of non-AIDS-defining malignancies in the HAART era: a clinico-epidemiological study
Dauby Nicolas,De Wit Stéphane,Delforge Marc,Necsoi Valentina
Journal of the International AIDS Society , 2011, DOI: 10.1186/1758-2652-14-16
Abstract: Background Non-AIDS-defining malignancies (NADM) are becoming a major cause of mortality in the era of highly active antiretroviral therapy. We wished to investigate the incidence, risks factors and outcome of NADM in an urban cohort. Methods We carried out an observational cohort of HIV patients with 12,746 patient-years of follow up between January 2002 and March 2009. Socio-demographics and clinical characteristics of patients diagnosed with NADM were retrospectively compared with the rest of the cohort. Causes of death and risk factors associated with NADM were assessed using logistic regression. Survival analyses were performed with Kaplan-Meier estimates. Cancer incidences were compared with those of the general population of the Brussels-Capital Region using the standardized incidence ratio (SIR). Results Forty-five NADM were diagnosed. At inclusion in the study, patients with NADM were older than patients without NADM (47 years vs. 38 years, p < 0.001), had a longer history of HIV infection (59 months vs. 39 months, p = 0.0174), a lower nadir CD4 count (110 cells/mm3 vs. 224 cells/mm3, p < 0.0001) and a higher rate of previous AIDS events (33% vs. 20%, p = 0.0455) and of hepatitis C virus co-infection (22.2% vs. 10%, p = 0.0149). In multivariate analysis, age over 45 at baseline (OR 3.25; 95% CI 1.70-6.22) and a nadir CD4 count of less than 200 cells/mm3 (OR 3.10; 95% CI 1.40-6.87) were associated with NADM. NADM were independently associated with higher mortality in the cohort (OR 14.79; 95% CI 6.95-31.49). Women with cancer, the majority of whom were of sub-Saharan African origin, had poorer survival compared with men. The SIR for both sexes were higher than expected for Hodgkin's lymphoma (17.78; 95% CI 6.49-38.71), liver cancers (8.73; 95% CI 2.35-22.34), anal cancers (22.67; 95% CI 8.28-49.34) and bladder cancers (3.79; 95% CI 1.02-9.70). The SIR for breast cancer was lower in women (SIR 0.29; 95% CI 0.06-0.85). Conclusions Age over 45 and a nadir CD4 count of less than 200 cells/mm3 were predictive of NADM in our cohort. Mortality was high, especially in sub-Saharan African women. Cancers with increased incidences were Hodgkin's lymphoma and anal, bladder and liver cancers in both sexes; women had a lower incidence of breast cancer.
Amount of Information Needed for Model Choice in Approximate Bayesian Computation
Michael Stocks, Mathieu Siol, Martin Lascoux, Stéphane De Mita
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099581
Abstract: Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.
Optophysiological Approach to Resolve Neuronal Action Potentials with High Spatial and Temporal Resolution in Cultured Neurons
Stéphane Pagès,Daniel C?té,Paul De Koninck
Frontiers in Cellular Neuroscience , 2011, DOI: 10.3389/fncel.2011.00020
Abstract: Cell to cell communication in the central nervous system is encoded into transient and local membrane potential changes (ΔVm). Deciphering the rules that govern synaptic transmission and plasticity entails to be able to perform Vm recordings throughout the entire neuronal arborization. Classical electrophysiology is, in most cases, not able to do so within small and fragile neuronal subcompartments. Thus, optical techniques based on the use of fluorescent voltage-sensitive dyes (VSDs) have been developed. However, reporting spontaneous or small ΔVm from neuronal ramifications has been challenging, in part due to the limited sensitivity and phototoxicity of VSD-based optical measurements. Here we demonstrate the use of water soluble VSD, ANNINE-6plus, with laser-scanning microscopy to optically record ΔVm in cultured neurons. We show that the sensitivity (>10% of fluorescence change for 100 mV depolarization) and time response (sub millisecond) of the dye allows the robust detection of action potentials (APs) even without averaging, allowing the measurement of spontaneous neuronal firing patterns. In addition, we show that back-propagating APs can be recorded, along distinct dendritic sites and within dendritic spines. Importantly, our approach does not induce any detectable phototoxic effect on cultured neurons. This optophysiological approach provides a simple, minimally invasive, and versatile optical method to measure electrical activity in cultured neurons with high temporal (ms) resolution and high spatial (μm) resolution.
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